Aptamer Selection by Darwinian Evolution

Abstract

Any technical object is defined by a structure and certain related properties, together with a function and a way of making it. A biological object is thus a biochemical structure, either organic or organically based, which possesses one or more biological properties (recognition, structure, transformation, etc.), which carries out a specific function, and which is produced by a biological process. A biological nano-object is a biological object with nanometric dimensions, from which we understand that it is a macromolecule or an assembly of such (diameter of a hemoglobin molecule 5.5 nm). By learning to understand and manipulate the enzymes that produce these macromolecules, biotechnology can today create or sculpt biological nanoobjects using fabrication processes that closely resemble natural mechanisms of synthesis, but which do not require the presence of a living being. Although these activities are recent and still somewhat limited, our mastery of the living tool box has already produced some entities with industrial prospects, including some artificial nano-objects with quite remarkable properties, unknown in nature. Among the biological macromolecules, the nucleic acids play a central role beecause they define both the species and the individual and provide the chemical support for heredity. They are also the only biological molecules we are able to reproduce identically by a simple and well understood enzyme mechanism, viz., the polymerase chain reaction (PCR) (see Chap. 15), which lends itself particularly well to mass production. The nucleic acids feature amongst the most widely used compounds in biology at the current time, e.g., as probes, amplification initiator, etc., as attested by the present market for oligonucleotides (short sequences of nucleic acids): 340 million dollars in 2003, with a predicted 776 million dollars in 2010. However, the use of nucleic acids is generally based on the canonical Watson–Crick pairing of nuclear bases, whose sequence encodes genetic information, while their wealth of structural potential remains virtually unexploited. In contrast, natural evolution has selected many RNA for their catalytic activities or for their ability to interact with proteins or other classes of molecules.